Enhanced ATV Viewer/Editor:

ATV is a wonderful tree viewer developed by Zmasek et al.. TreeFam eATV improved ATV by adding tree editting functions and applying better color schemes. Also we add a function to it in order to show Ka/Ks ratio. The enhanced ATV (FGF eATV) can be downloaded here(require Java 1.4 or higher). As the original ATV and TreeFam eATV is distributed under GPL (GNU General Public License), FGF eATV is also covered by GPL.

NJTREE: a Versatile Tree Builder

NJTREE is the core engine of TreeFam database. It is a constrained neighbour-joining tree builder and also capable of duplication/loss inference, tree merge, alignment filtering, tree plotting, format converting and many other routines used in TreeFam. NJTREE is distributed under GPL. Source codes can be freely downloaded as njtree-current.tar.gz. Precompiled binary files can also be found at njtree-bin.tar.gz.

KaKs_Calculator

KaKs_Calculator is a program that calculates nonsynonymous (Ka) and synonymous (Ks) substitution rates through model selection and model averaging, which attempt to include as much features as needed for accurately capturing evolutionary information in protein-coding sequences. In addition, several existing methods for calculating Ka and Ks are also incorporated into KaKs_Calculator. Download KaKs_Calculator1.2 (including source codes, compiled executables on AIX/IRIX/Solaris and setup application on Windows)

BioEdit

BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP. An intuitive multiple document interface with convenient features makes alignment and manipulation of sequences relatively easy on your desktop computer. Several sequence manipulation and analysis options and links to external anaylsis programs facilitate a working environment which allows you to view and manipulate sequences with simple point-and-click operations.

MEGA 3.1: Molecular Evolutionary Genetics Analysis

MEGA is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses by Sudhir Kumar, Koichiro Tamura, Masatoshi Nei, MEGA can be download here.

Phylogenetic Analysis by Maximum Likelihood (PAML)

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/MAC OS X, and executables are provided for MS Windows. can be freely download here.

PHYLIP

PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. These Web pages, by Joe Felsenstein of the Department of Genome Sciences and the Department of Biology at the University of Washington, contain information on PHYLIP and ways to transfer the executables, source code and documentation to your computer.

K-Estimator 6.1

A program to estimate the number of synonymous (Ks) and nonsynonymous substitutions (Ka) per site and the confidence intervals by Monte Carlo simulations. Download here.